Try drydocking the turtle for about 8 hours a day. That should help.
Also...Zoo Med makes a Sulfa dip for turtles. I have had good luck with that.
Soak the turtle in it for a couple of hours, then let the turtle dry out completely.
Repeat this for about a week. Also, you might want to check the pH of the water. Too much alkaline can cause shell problems in some turtles. Where I live, the tap water itself has a high pH.
So I add acids to the water when changing water just to bring it to neutral.
All of these are easily accomplished.
Acid, drying, sulfa. None of these allow for an enviornment for fungus to grow.
Good Luck
Bob